Project / group specific documentation at the bottom of this page...

Documentation relevant for multiple groups / projects

• RequestAccount? - How to request an account for access to GCC maintained infrastructure
• DataSharing? - How to up-/download data via SFTP
• TransparentMultiHopSSH? - How to connect via the proxy

Documentation on the MOLGENIS software suite

• Developer Manual - OUTDATED in progress of migration to github
• using xQTL workbench for multi-level QTL mapping
• Tracking Code - Add app statistics tracking code
• Using SORTA - How to deploy SORTA in tomcat 7

Documentation on the MOLGENIS/compute

• MOLGENIS/compute Start page featuring code, manuals and presentations.
• DeployDependencies? - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)

GCC Cloud VMs / Jenkins / Tomcat / MySQL / WordPress

• Molgenis Servers? - List of all VMs in our cloud.
• Create Molgenis VM - How to request and configure a new Molgenis VM cloned from the 'molgenis gold' template.
• Install SOP / Tomcat7 - How to deploy Tomcat7 on a Molgenis VM.
• Install SOP / Tomcat Auth - How to add Tomcat 7 basic login authentication.
• Install SOP / Deploy MOLGENIS via Jenkins - How to deploy MOLGENIS on a VM using Jenkins.
• Molgenis VM multiple certificates - Use Molgenis VM with multiple certificates.
• MySQL setup?
• SOP Nightlies? - How to create a nightly build
• SOP WordPress - How to manage WordPress websites

High Performance Computing (HPC) infra

• version 1.x (Deprecated) - How to compute on the GCC cluster
• version 2.x (New!) - How to compute on the Calculon, Zinc-Finger and Leucine-Zipper Clusters
• Overview? - Description of the differences between the 1.x and 2.x HPC environments

New employee

• SOP new Employee (employee) - Manual for employee
• SOP New Employee (team) - Manual for team
• IntellijTips - Tips for using IntelliJ

Documentation for specific projects / groups

Internal GCC SOPs

• How to print the scrum cards
• Connect to Xerox printers for Mac OS X
• SOPs - Most used Standard Operating Procedures (authorized users only)
• Intranet - List of all SOPs; common and obscure (authorized users only)
• GccSopMolgenisRelease - How to create a MOLGENIS release
• GccSopSystemsGeneticsRelease - How to create a Systems Genetics release

IBD SOP

• Retreive and convert IBD Stage data

LifeLines SOPs

• SopConvertLifeLinesGenoData - how to prepare the geno data from release 3 + imputation (2 sets)
• GccSopLifelinesDeploy - How to deploy Lifelines

BBMRI SOPs

• SopUpdateBbmriApp - How to Update BBMRIApp (Legacy SOP)

Liferay SOPs

• GccSopLiferayBBMRI_NL - How to configure and install Liferay (SOP)

ASE SOP

• GccSopAseDeploy - How to deploy the ASE site

PALGA SOP

• GccSopPALGADeploy - How to deploy PALGA

PhD roadmap

• GccPhdChao - Chao`s roadmap and corresponding stories